This article has been reviewed according to Science X's editorial process and policies. Editors have highlighted the following attributes while ensuring the content's credibility: A genome contains all of the DNA of every living organism, but its contents don't stop there—most of these structures also contain snippets of DNA that can copy and paste themselves to "infect" a genome, expanding its size. Precisely why that happens remains a mystery.
Researchers have created a new computational tool that works from an inferred ancestral point and evolves forward to the modern-day genome to trace the insertion and deletion dynamics of these "jumping genes," known as transposable elements. Scientists at The Ohio State University who study how transposable elements, also called transposons or TEs, may have altered gene functions over time were looking for the best way to trace that evolutionary history, so they created the simulator they needed to do the work. "In the timescale of millions or tens of millions of years, transposon activity is really dense.
There are many, many transposon insertions and deletions to the genome and from the genome," said senior study author Shujun Ou, assistant professor of molecular genetics at Ohio State. "We want to use the footprint of that activity to study what may have happened in the past because we'll never know for sure, but we can infer what may be the case in terms of transposon activity." Their initial findings from a case study on fungal genomes hinted at how bursts of TE insertions were followed by deletions, suggesting the fungus fought back to suppress further insertions. Ou and colleagues describe the PrinTE simulator on Nov. 2, 2026, in Nature Communications.
The corn genome is perhaps the best-known example of the transposon effect on genome expansion: Up to 85% of its genome consists of jumping genes, said first author Christopher Benson, a postdoctoral scholar in Ou's lab. "These are big components of a genome that maybe don't necessarily have a noticeable impact, but they exist. They're functioning in the background in these ways that we're still trying to understand," Benson said.
"But one thing that they do is impact genome size evolution heavily because they often insert as a copy-and-paste. You have the original copy and the duplicated copy. So if you do this tons of times, you get a really enormous genome." This phenomenon is known as the genome size paradox: Plants with major differences in genome size function in the same way.
"Is there any value of having a genome that's bigger or smaller? It's paradoxical because if genome size is important, the larger genome plants must have more actual function or a more complicated structure," Ou said. "But in observation, they don't." Ou and Benson designed PrinTE as an enhancement of a previous tool called TEGenomeSimulator, which provides a snapshot of transposon infection of a genome at a single point in time.
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